rs881372

Variant names:

• chr6-40882138-G-A
• rs881372
• ENST00000716631.1:n.712+884C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-40882138-G-A
• chr6-40882138-G-C

Variant summary

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

The ENST00000716631.1(ENSG00000293636):​n.712+884C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,066 control chromosomes in the GnomAD database, including 2,332 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 0.17 (2332 hom., cov: 32)
• Consequence: ENSG00000293636 ENST00000716631.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660
• Publications: 1 publications found

Genes affected

ENSG00000293636 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929555	NR_110873.1	n.676+884C>T		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293636	ENST00000716631.1	n.712+884C>T		intron_variant	Intron 6 of 8
ENSG00000293636	ENST00000716633.1	n.919+884C>T		intron_variant	Intron 7 of 7
ENSG00000293636	ENST00000740548.1	n.666+884C>T		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26428 AN: 151948 Hom.: 2329 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.0670

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.174 AC: 26448 AN: 152066 Hom.: 2332 Cov.: 32 AF XY: 0.174 AC XY: 12946 AN XY: 74328

African (AFR) AF: 0.188 AC: 7799 AN: 41454

American (AMR) AF: 0.199 AC: 3044 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 409 AN: 3470

East Asian (EAS) AF: 0.191 AC: 983 AN: 5152

South Asian (SAS) AF: 0.186 AC: 896 AN: 4822

European-Finnish (FIN) AF: 0.184 AC: 1952 AN: 10592

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10900 AN: 67974

Other (OTH) AF: 0.176 AC: 370 AN: 2108

Alfa AF: 0.175 Hom.: 328

Bravo AF: 0.175

Asia WGS AF: 0.172 AC: 598 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.57
PhyloP100		-0.066

Splicing

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

Other links and lift over

dbSNP: rs881372; hg19: chr6-40849877;