chr4-28549715-A-T

Position:

• chr4-28549715-A-T

Variant summary

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

The ENST00000509416.1(ENSG00000250064):​n.403-28201A>T 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 0.123 in 151,896 control chromosomes in the GnomAD database, including 1,373 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 0.12 (1373 hom., cov: 32)
• Consequence: ENST00000509416.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374557	XR_001741640.2	n.891-28201A>T		intron_variant, non_coding_transcript_variant
LOC105374558	XR_925528.3	n.332-26559T>A		intron_variant, non_coding_transcript_variant
LOC105374557	XR_001741639.2	n.301-28201A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000509416.1	n.403-28201A>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18743 AN: 151778 Hom.: 1375 Cov.: 32

Gnomad AFR AF: 0.0538

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.132

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.123 AC: 18736 AN: 151896 Hom.: 1373 Cov.: 32 AF XY: 0.126 AC XY: 9365 AN XY: 74252

Gnomad4 AFR AF: 0.0536

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.129

Alfa AF: 0.131 Hom.: 183

Bravo AF: 0.118

Asia WGS AF: 0.183 AC: 635 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.32
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17642174; hg19: chr4-28551337;