rs195517

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000692859.2(ENSG00000289376):​n.223-18243C>T variant causes a intron, non coding transcript 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: ENST00000692859.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC124901385	XR_007059720.1	n.961+6057C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000692859.2	n.223-18243C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.0195

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.359

Alfa AF: 0.196 Hom.: 368

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

Splicing

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

Publications

LitVar

Other links and lift over

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