rs1962736

Positions:

• chr16-1275970-G-A
• chr16-1275970-G-T

Variant summary

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

The ENST00000562876.2(ENSG00000261564):​n.500C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,846 control chromosomes in the GnomAD database, including 20,162 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 0.50 (20162 hom., cov: 32)
• Consequence: ENST00000562876.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000562876.2	n.500C>T		non_coding_transcript_exon_variant	3/5

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76390 AN: 151728 Hom.: 20145 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.503 AC: 76446 AN: 151846 Hom.: 20162 Cov.: 32 AF XY: 0.518 AC XY: 38407 AN XY: 74206

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.921

Gnomad4 SAS AF: 0.753

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.475

Alfa AF: 0.476 Hom.: 17917

Bravo AF: 0.498

Asia WGS AF: 0.764 AC: 2653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.53
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1962736; hg19: chr16-1325971;