chr21-37207613-G-A

Variant names:

• chr21-37207613-G-A
• rs2835667
• ENST00000787142.1:n.208-7988C>T

Variant summary

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

The ENST00000787142.1(ENSG00000302472):​n.208-7988C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 152,048 control chromosomes in the GnomAD database, including 22,191 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 0.53 (22191 hom., cov: 32)
• Consequence: ENSG00000302472 ENST00000787142.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192
• Publications: 14 publications found

Genes affected

ENSG00000302472 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000787142.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302472	ENST00000787142.1		n.208-7988C>T		intron	N/A
	ENSG00000302472	ENST00000787143.1		n.186-9941C>T		intron	N/A
	ENSG00000302472	ENST00000787144.1		n.212-6986C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80843 AN: 151930 Hom.: 22159 Cov.: 32

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.532 AC: 80922 AN: 152048 Hom.: 22191 Cov.: 32 AF XY: 0.535 AC XY: 39746 AN XY: 74328

African (AFR) AF: 0.642 AC: 26636 AN: 41470

American (AMR) AF: 0.577 AC: 8828 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1394 AN: 3466

East Asian (EAS) AF: 0.573 AC: 2957 AN: 5164

South Asian (SAS) AF: 0.577 AC: 2782 AN: 4822

European-Finnish (FIN) AF: 0.530 AC: 5604 AN: 10574

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.458 AC: 31106 AN: 67942

Other (OTH) AF: 0.546 AC: 1156 AN: 2116

Alfa AF: 0.470 Hom.: 21427

Bravo AF: 0.536

Asia WGS AF: 0.597 AC: 2077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.40
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs2835667; hg19: chr21-38579914;