rs9375085

chr6-98024688-G-Cchr6-98024688-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000656098.1(ENSG00000271860):n.1315+55222G>C 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 0.117 in 169,920 control chromosomes in the GnomAD database, including 1,241 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 0.12 (1174 hom., cov: 32)
  • Exomes 𝑓: 0.092 (67 hom.)
• Consequence: ENST00000656098.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000656098.1	n.1315+55222G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18174 AN: 151874 Hom.: 1172 Cov.: 32

Gnomad AFR AF: 0.0921

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0867

Gnomad MID AF: 0.0935

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.133

GnomAD4 exome AF: 0.0923 AC: 1655 AN: 17926 Hom.: 67 AF XY: 0.0941 AC XY: 807 AN XY: 8576

Gnomad4 AFR exome AF: 0.0750

Gnomad4 AMR exome AF: 0.250

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.250

Gnomad4 SAS exome AF: 0.159

Gnomad4 FIN exome AF: 0.0906

Gnomad4 NFE exome AF: 0.140

Gnomad4 OTH exome AF: 0.102

GnomAD4 genome AF: 0.120 AC: 18176 AN: 151994 Hom.: 1174 Cov.: 32 AF XY: 0.120 AC XY: 8903 AN XY: 74292

Gnomad4 AFR AF: 0.0919

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0867

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.132

Alfa AF: 0.0567 Hom.: 67

Bravo AF: 0.129

Asia WGS AF: 0.140 AC: 487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
Cadd	Benign	16
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9375085; hg19: chr6-98472564; COSMIC: COSV71816442;