chr6-43751654-G-T

Variant names:

• chr6-43751654-G-T
• rs9394963
• ENST00000770040.1:n.95+6889C>A

Variant summary

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

The ENST00000770040.1(ENSG00000236961):​n.95+6889C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 152,092 control chromosomes in the GnomAD database, including 8,386 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 0.33 (8386 hom., cov: 33)
• Consequence: ENSG00000236961 ENST00000770040.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 11 publications found

Genes affected

ENSG00000236961 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.355 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
ENSG00000236961	ENST00000770040.1	n.95+6889C>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49938 AN: 151974 Hom.: 8373 Cov.: 33

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.329 AC: 49996 AN: 152092 Hom.: 8386 Cov.: 33 AF XY: 0.326 AC XY: 24260 AN XY: 74342

African (AFR) AF: 0.292 AC: 12113 AN: 41484

American (AMR) AF: 0.253 AC: 3862 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1450 AN: 3468

East Asian (EAS) AF: 0.237 AC: 1226 AN: 5174

South Asian (SAS) AF: 0.368 AC: 1778 AN: 4826

European-Finnish (FIN) AF: 0.379 AC: 4008 AN: 10566

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24405 AN: 67968

Other (OTH) AF: 0.317 AC: 671 AN: 2114

Alfa AF: 0.348 Hom.: 14699

Bravo AF: 0.316

Asia WGS AF: 0.291 AC: 1013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.2
DANN	Benign	0.70
PhyloP100		0.077

Splicing

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

Other links and lift over

dbSNP: rs9394963; hg19: chr6-43719391;