8-62197100-G-T

Variant names:

• chr8-62197100-G-T
• rs1483172
• ENST00000649904.1:n.424-1507C>A

Variant summary

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

The ENST00000649904.1(ENSG00000285971):​n.424-1507C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 152,002 control chromosomes in the GnomAD database, including 26,967 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 0.59 (26967 hom., cov: 32)
• Consequence: ENSG00000285971 ENST00000649904.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173
• Publications: 1 publications found

Genes affected

ENSG00000285971 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649904.1. 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
	ENSG00000285971	ENST00000649904.1		n.424-1507C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89411 AN: 151884 Hom.: 26911 Cov.: 32

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.589 AC: 89528 AN: 152002 Hom.: 26967 Cov.: 32 AF XY: 0.588 AC XY: 43657 AN XY: 74284

African (AFR) AF: 0.709 AC: 29399 AN: 41472

American (AMR) AF: 0.594 AC: 9076 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 1934 AN: 3470

East Asian (EAS) AF: 0.726 AC: 3735 AN: 5148

South Asian (SAS) AF: 0.601 AC: 2895 AN: 4820

European-Finnish (FIN) AF: 0.454 AC: 4790 AN: 10550

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.528 AC: 35849 AN: 67958

Other (OTH) AF: 0.593 AC: 1253 AN: 2112

Alfa AF: 0.534 Hom.: 11084

Bravo AF: 0.609

Asia WGS AF: 0.662 AC: 2303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.43
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs1483172; hg19: chr8-63109659;