rs945131

Variant names:

• chr6-43748257-A-G
• rs945131
• ENST00000770040.1:n.95+10286T>C

Variant summary

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

The ENST00000770040.1(ENSG00000236961):​n.95+10286T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 152,160 control chromosomes in the GnomAD database, including 15,467 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 0.44 (15467 hom., cov: 33)
• Consequence: ENSG00000236961 ENST00000770040.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190
• Publications: 8 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.505 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+10286T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67354 AN: 152042 Hom.: 15458 Cov.: 33

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.443 AC: 67399 AN: 152160 Hom.: 15467 Cov.: 33 AF XY: 0.437 AC XY: 32532 AN XY: 74386

African (AFR) AF: 0.361 AC: 15001 AN: 41510

American (AMR) AF: 0.353 AC: 5392 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2112 AN: 3472

East Asian (EAS) AF: 0.243 AC: 1257 AN: 5178

South Asian (SAS) AF: 0.438 AC: 2112 AN: 4820

European-Finnish (FIN) AF: 0.499 AC: 5284 AN: 10592

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.509 AC: 34608 AN: 67982

Other (OTH) AF: 0.440 AC: 928 AN: 2110

Alfa AF: 0.485 Hom.: 82366

Bravo AF: 0.429

Asia WGS AF: 0.342 AC: 1189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.25
DANN	Benign	0.40
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs945131; hg19: chr6-43715994;