rs7612441

Positions:

• chr3-66597738-C-T

Variant summary

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

The XR_940934.2(LOC105377141):​n.77-7991C>T 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 0.226 in 152,078 control chromosomes in the GnomAD database, including 4,533 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 0.23 (4533 hom., cov: 32)
• Consequence: LOC105377141 XR_940934.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635

Genes affected

LOC105377141 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377141	XR_940934.2	n.77-7991C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34438 AN: 151960 Hom.: 4535 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.0462

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.226 AC: 34442 AN: 152078 Hom.: 4533 Cov.: 32 AF XY: 0.223 AC XY: 16569 AN XY: 74336

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.0463

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.240

Alfa AF: 0.287 Hom.: 8695

Bravo AF: 0.221

Asia WGS AF: 0.0980 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.7
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7612441; hg19: chr3-66648162;