rs195517

Variant names:

• chr6-115920421-G-A
• rs195517
• ENST00000692859.3:n.269-18243C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-115920421-G-A
• chr6-115920421-G-T

Variant summary

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

The ENST00000692859.3(ENSG00000289376):​n.269-18243C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 151,832 control chromosomes in the GnomAD database, including 8,783 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 (8783 hom., cov: 32)
• Consequence: ENSG00000289376 ENST00000692859.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329
• Publications: 3 publications found

Genes affected

ENSG00000289376 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901385	XR_007059720.1	n.961+6057C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289376	ENST00000692859.3	n.269-18243C>T		intron_variant	Intron 1 of 1
ENSG00000289376	ENST00000848637.1	n.961+6057C>T		intron_variant	Intron 1 of 1
ENSG00000289376	ENST00000848638.1	n.961+6057C>T		intron_variant	Intron 1 of 1
ENSG00000289376	ENST00000848639.1	n.30+6057C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50004 AN: 151714 Hom.: 8769 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.0193

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.330 AC: 50048 AN: 151832 Hom.: 8783 Cov.: 32 AF XY: 0.321 AC XY: 23792 AN XY: 74178

African (AFR) AF: 0.383 AC: 15872 AN: 41388

American (AMR) AF: 0.281 AC: 4280 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1338 AN: 3460

East Asian (EAS) AF: 0.0195 AC: 101 AN: 5172

South Asian (SAS) AF: 0.225 AC: 1085 AN: 4818

European-Finnish (FIN) AF: 0.250 AC: 2628 AN: 10520

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23736 AN: 67916

Other (OTH) AF: 0.359 AC: 758 AN: 2110

Alfa AF: 0.204 Hom.: 416

Bravo AF: 0.335

Asia WGS AF: 0.143 AC: 500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.67
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs195517; hg19: chr6-116241584; COSMIC: COSV60271211;