7-24197136-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000439839.1(ENSG00000228944):n.160-107G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 151,732 control chromosomes in the GnomAD database, including 9,656 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.33 (9656 hom., cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENST00000439839.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986777	XR_001745132.2	n.210-107G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000439839.1	n.160-107G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50573 AN: 151614 Hom.: 9645 Cov.: 31

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.312

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.334 AC: 50615 AN: 151732 Hom.: 9656 Cov.: 31 AF XY: 0.339 AC XY: 25138 AN XY: 74128

Gnomad4 AFR AF: 0.507

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.309

Alfa AF: 0.291 Hom.: 1189

Bravo AF: 0.349

Asia WGS AF: 0.440 AC: 1530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.1
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs156293; hg19: chr7-24236755;