rs7770216

Variant names:

• chr6-31372834-G-T
• rs7770216
• ENST00000649421.1:n.275-2049G>T

Variant summary

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

The ENST00000649421.1(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 ENST00000649421.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469

Genes affected

ENSG00000285647 (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 = 0.385 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	ENST00000649421.1	n.275-2049G>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

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.377

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.244

Alfa AF: 0.204 Hom.: 719

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7770216; hg19: chr6-31340611;