chr6-170177401-G-A

Position:

• chr6-170177401-G-A

Variant summary

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

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 0.089 (536 hom., cov: 20)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.983

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.170177401G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000230960	ENST00000691159.1	n.357+8406C>T		intron_variant
ENSG00000230960	ENST00000701993.1	n.382+8337C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0886 AC: 7673 AN: 86598 Hom.: 534 Cov.: 20

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.0103

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0449

Gnomad EAS AF: 0.00216

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0469

Gnomad MID AF: 0.183

Gnomad NFE AF: 0.0889

Gnomad OTH AF: 0.0936

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

GnomAD4 genome AF: 0.0886 AC: 7678 AN: 86658 Hom.: 536 Cov.: 20 AF XY: 0.0875 AC XY: 3659 AN XY: 41834

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0449

Gnomad4 EAS AF: 0.00217

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.0469

Gnomad4 NFE AF: 0.0889

Gnomad4 OTH AF: 0.0944

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.5
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7453655; hg19: chr6-170492625;