rs6657442

Positions:

• chr1-196868930-T-C

Variant summary

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

The ENST00000649395.1(ENSG00000285986):​n.426+10526T>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 0.193 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: ENST00000649395.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000649395.1	n.426+10526T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0582

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.211

Alfa AF: 0.204 Hom.: 1595

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs6657442; hg19: chr1-196838060;