rs2115869

Variant names:

• chr6-160786860-G-A
• rs2115869

Your query was ambiguous. Multiple possible variants found:

• chr6-160786860-G-A
• chr6-160786860-G-C

Variant summary

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

The variant allele was found at a frequency of 0.403 in 151,952 control chromosomes in the GnomAD database, including 12,759 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 0.40 (12759 hom., cov: 32)
• Consequence: LOC107986665 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.84
• Publications: 2 publications found

Genes affected

LOC107986665 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986665		n.160786860G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303572	ENST00000795697.1	n.244-10419C>T		intron_variant	Intron 1 of 2
ENSG00000303572	ENST00000795698.1	n.218-10419C>T		intron_variant	Intron 1 of 2
ENSG00000303572	ENST00000795699.1	n.251-10419C>T		intron_variant	Intron 1 of 1
ENSG00000303572	ENST00000795700.1	n.269-3620C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61154 AN: 151834 Hom.: 12744 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.403 AC: 61200 AN: 151952 Hom.: 12759 Cov.: 32 AF XY: 0.406 AC XY: 30145 AN XY: 74278

African (AFR) AF: 0.418 AC: 17335 AN: 41424

American (AMR) AF: 0.530 AC: 8083 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1097 AN: 3466

East Asian (EAS) AF: 0.606 AC: 3133 AN: 5168

South Asian (SAS) AF: 0.412 AC: 1985 AN: 4814

European-Finnish (FIN) AF: 0.319 AC: 3366 AN: 10556

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24860 AN: 67942

Other (OTH) AF: 0.405 AC: 855 AN: 2112

Alfa AF: 0.285 Hom.: 836

Bravo AF: 0.420

Asia WGS AF: 0.464 AC: 1611 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.38
DANN	Benign	0.59
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs2115869; hg19: chr6-161207892; COSMIC: COSV60299221;