rs6532197

Variant names:

• chr4-89876150-A-G
• rs6532197
• ENST00000776860.1:n.208+22203T>C

Variant summary

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

The ENST00000776860.1(ENSG00000301182):​n.208+22203T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,222 control chromosomes in the GnomAD database, including 3,013 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 0.16 (3013 hom., cov: 32)
• Consequence: ENSG00000301182 ENST00000776860.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116
• Publications: 30 publications found

Genes affected

ENSG00000301182 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 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
ENSG00000301182	ENST00000776860.1	n.208+22203T>C		intron_variant	Intron 1 of 1
ENSG00000301182	ENST00000776861.1	n.182+19169T>C		intron_variant	Intron 1 of 1
ENSG00000301182	ENST00000776862.1	n.80+19169T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23900 AN: 152104 Hom.: 3002 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.0560

Gnomad AMR AF: 0.0902

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0569

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0705

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.157 AC: 23945 AN: 152222 Hom.: 3013 Cov.: 32 AF XY: 0.154 AC XY: 11453 AN XY: 74416

African (AFR) AF: 0.342 AC: 14184 AN: 41500

American (AMR) AF: 0.0900 AC: 1378 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 381 AN: 3470

East Asian (EAS) AF: 0.316 AC: 1631 AN: 5164

South Asian (SAS) AF: 0.111 AC: 537 AN: 4826

European-Finnish (FIN) AF: 0.0569 AC: 604 AN: 10620

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.0705 AC: 4796 AN: 68018

Other (OTH) AF: 0.159 AC: 336 AN: 2114

Alfa AF: 0.102 Hom.: 5680

Bravo AF: 0.169

Asia WGS AF: 0.229 AC: 795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.0
DANN	Benign	0.58
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs6532197; hg19: chr4-90797301;