6-170177401-G-C

Position:

• chr6-170177401-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

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 0.018 (180 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).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0177 (1536/86712) while in subpopulation NFE AF= 0.0257 (1036/40324). AF 95% confidence interval is 0.0244. There are 180 homozygotes in gnomad4. There are 693 alleles in male gnomad4 subpopulation. Median coverage is 20. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 180 gene

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0177 AC: 1537 AN: 86652 Hom.: 180 Cov.: 20

Gnomad AFR AF: 0.00993

Gnomad AMI AF: 0.0226

Gnomad AMR AF: 0.0152

Gnomad ASJ AF: 0.0207

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0108

Gnomad FIN AF: 0.00793

Gnomad MID AF: 0.0352

Gnomad NFE AF: 0.0257

Gnomad OTH AF: 0.0168

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

GnomAD4 genome AF: 0.0177 AC: 1536 AN: 86712 Hom.: 180 Cov.: 20 AF XY: 0.0166 AC XY: 693 AN XY: 41854

Gnomad4 AFR AF: 0.00991

Gnomad4 AMR AF: 0.0152

Gnomad4 ASJ AF: 0.0207

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0104

Gnomad4 FIN AF: 0.00793

Gnomad4 NFE AF: 0.0257

Gnomad4 OTH AF: 0.0167

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.0
DANN	Benign	0.35

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;