19-42326085-A-T

Position:

• chr19-42326085-A-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001271938.2(MEGF8):​c.-159A>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00419 in 1,224,890 control chromosomes in the GnomAD database, including 162 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.018 (91 hom., cov: 32)
  • Exomes 𝑓: 0.0022 (71 hom.)
• Consequence: MEGF8 NM_001271938.2 5_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.108

Genes affected

MEGF8 (HGNC:3233): (multiple EGF like domains 8) The protein encoded by this gene is a single-pass type I membrane protein of unknown function that contains several EGF-like domains, Kelch repeats, and PSI domains. Defects in this gene are a cause of Carpenter syndrome 2. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 19-42326085-A-T is Benign according to our data. Variant chr19-42326085-A-T is described in ClinVar as [Benign]. Clinvar id is 1283337.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MEGF8	NM_001271938.2	c.-159A>T		5_prime_UTR_variant	1/42	ENST00000251268.11
MEGF8	NM_001410.3	c.-159A>T		5_prime_UTR_variant	1/41

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MEGF8	ENST00000251268.11	c.-159A>T		5_prime_UTR_variant	1/42	5	NM_001271938.2	A2
MEGF8	ENST00000334370.8	c.-159A>T		5_prime_UTR_variant	1/41	1		P2
MEGF8	ENST00000378073.5	c.-7244A>T		5_prime_UTR_variant	1/41	5

Frequencies

GnomAD3 genomes AF: 0.0181 AC: 2746 AN: 152088 Hom.: 83 Cov.: 32

Gnomad AFR AF: 0.0612

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00831

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.000618

Gnomad OTH AF: 0.0148

GnomAD4 exome AF: 0.00220 AC: 2355 AN: 1072684 Hom.: 71 Cov.: 15 AF XY: 0.00210 AC XY: 1090 AN XY: 519632

Gnomad4 AFR exome AF: 0.0733

Gnomad4 AMR exome AF: 0.00511

Gnomad4 ASJ exome AF: 0.00135

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000299

Gnomad4 FIN exome AF: 0.0000269

Gnomad4 NFE exome AF: 0.000452

Gnomad4 OTH exome AF: 0.00636

GnomAD4 genome AF: 0.0183 AC: 2782 AN: 152206 Hom.: 91 Cov.: 32 AF XY: 0.0180 AC XY: 1340 AN XY: 74408

Gnomad4 AFR AF: 0.0619

Gnomad4 AMR AF: 0.00830

Gnomad4 ASJ AF: 0.00115

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000618

Gnomad4 OTH AF: 0.0147

Alfa AF: 0.0121 Hom.: 9

Bravo AF: 0.0209

Asia WGS AF: 0.0130 AC: 46 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 29, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.5
DANN	Benign	0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs111536758; hg19: chr19-42830237;