rs6657442

Variant names:

• chr1-196868930-T-C
• rs6657442

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.193 in 150,594 control chromosomes in the GnomAD database, including 3,871 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 0.19 (3871 hom., cov: 31)
• Consequence: LOC100996886 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115
• Publications: 10 publications found

Genes affected

LOC100996886 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100996886		n.196868930T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285986	ENST00000649395.1	n.426+10526T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29081 AN: 150480 Hom.: 3859 Cov.: 31

Gnomad AFR AF: 0.0584

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.193 AC: 29105 AN: 150594 Hom.: 3871 Cov.: 31 AF XY: 0.199 AC XY: 14629 AN XY: 73490

African (AFR) AF: 0.0582 AC: 2379 AN: 40856

American (AMR) AF: 0.314 AC: 4735 AN: 15074

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 894 AN: 3464

East Asian (EAS) AF: 0.374 AC: 1896 AN: 5068

South Asian (SAS) AF: 0.250 AC: 1199 AN: 4792

European-Finnish (FIN) AF: 0.271 AC: 2807 AN: 10360

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14599 AN: 67686

Other (OTH) AF: 0.211 AC: 442 AN: 2090

Alfa AF: 0.203 Hom.: 1813

Bravo AF: 0.190

Asia WGS AF: 0.327 AC: 1134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.9
DANN	Benign	0.19
PhyloP100		0.12
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs6657442; hg19: chr1-196838060;