chr6-31372834-G-T

Variant names:

• chr6-31372834-G-T
• rs7770216
• ENST00000649421.2:n.275-2049G>T

Variant summary

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

The ENST00000649421.2(ENSG00000285647):​n.275-2049G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 150,876 control chromosomes in the GnomAD database, including 4,479 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 0.22 (4479 hom., cov: 32)
• Consequence: ENSG00000285647 ENST00000649421.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469
• Publications: 19 publications found

Genes affected

ENSG00000285647 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.385 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
ENSG00000285647	ENST00000649421.2	n.275-2049G>T		intron_variant	Intron 1 of 1
ENSG00000298426	ENST00000755446.1	n.327-9146G>T		intron_variant	Intron 1 of 1
ENSG00000285647	ENST00000755530.1	n.203-2049G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.224 AC: 33797 AN: 150768 Hom.: 4479 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.224 AC: 33810 AN: 150876 Hom.: 4479 Cov.: 32 AF XY: 0.231 AC XY: 16999 AN XY: 73608

African (AFR) AF: 0.230 AC: 9510 AN: 41342

American (AMR) AF: 0.215 AC: 3207 AN: 14900

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 735 AN: 3468

East Asian (EAS) AF: 0.400 AC: 2023 AN: 5058

South Asian (SAS) AF: 0.377 AC: 1737 AN: 4608

European-Finnish (FIN) AF: 0.206 AC: 2143 AN: 10398

Middle Eastern (MID) AF: 0.286 AC: 83 AN: 290

European-Non Finnish (NFE) AF: 0.202 AC: 13675 AN: 67806

Other (OTH) AF: 0.244 AC: 513 AN: 2100

Alfa AF: 0.205 Hom.: 1056

Bravo AF: 0.223

Asia WGS AF: 0.331 AC: 1130 AN: 3406

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.9
DANN	Benign	0.25
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs7770216; hg19: chr6-31340611;