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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000692859.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289376	ENST00000692859.3		n.269-18243C>T		intron	N/A
	ENSG00000289376	ENST00000848637.1		n.961+6057C>T		intron	N/A
	ENSG00000289376	ENST00000848638.1		n.961+6057C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs195517;

hg19: chr6-116241584;

COSMIC: COSV60271211;