6-31422633-T-C

Variant names:

• chr6-31422633-T-C
• rs2516448
• ENST00000673857.1:n.62+21870T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000673857.1(ENSG00000288587):​n.62+21870T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 151,594 control chromosomes in the GnomAD database, including 32,162 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 0.64 (32162 hom., cov: 31)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 50 publications found

Genes affected

ENSG00000288587 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288587	ENST00000673857.1	n.62+21870T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97042 AN: 151478 Hom.: 32118 Cov.: 31

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.799

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.641 AC: 97141 AN: 151594 Hom.: 32162 Cov.: 31 AF XY: 0.651 AC XY: 48282 AN XY: 74114

African (AFR) AF: 0.702 AC: 28925 AN: 41204

American (AMR) AF: 0.781 AC: 11852 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2843 AN: 3460

East Asian (EAS) AF: 0.786 AC: 4048 AN: 5150

South Asian (SAS) AF: 0.797 AC: 3842 AN: 4818

European-Finnish (FIN) AF: 0.600 AC: 6323 AN: 10546

Middle Eastern (MID) AF: 0.791 AC: 231 AN: 292

European-Non Finnish (NFE) AF: 0.545 AC: 37045 AN: 67926

Other (OTH) AF: 0.726 AC: 1529 AN: 2106

Alfa AF: 0.582 Hom.: 70671

Bravo AF: 0.658

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.46
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2516448; hg19: chr6-31390410;