rs2462686

Positions:

• chr7-45942861-T-C

Variant summary

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

The ENST00000664963.1(ENSG00000237471):​n.432+1981T>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 0.281 in 152,084 control chromosomes in the GnomAD database, including 6,344 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 0.28 (6344 hom., cov: 32)
• Consequence: ENST00000664963.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102723446	XR_001745202.2	n.432+1981T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000664963.1	n.432+1981T>C		intron_variant, non_coding_transcript_variant
	ENST00000658576.1	n.164+1981T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42725 AN: 151966 Hom.: 6334 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.0350

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.281 AC: 42774 AN: 152084 Hom.: 6344 Cov.: 32 AF XY: 0.277 AC XY: 20628 AN XY: 74346

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.0351

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.302

Alfa AF: 0.305 Hom.: 1654

Bravo AF: 0.275

Asia WGS AF: 0.225 AC: 781 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2462686; hg19: chr7-45982460;