rs972283

Positions:

• chr7-130782095-A-G
• chr7-130782095-A-T

Variant summary

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

The XR_927978.3(LOC105375508):​n.178+44105A>G 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 0.634 in 152,002 control chromosomes in the GnomAD database, including 32,010 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 0.63 (32010 hom., cov: 31)
• Consequence: LOC105375508 XR_927978.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792

Genes affected

LOC105375508 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375508	XR_927978.3	n.178+44105A>G		intron_variant, non_coding_transcript_variant
LOC105375508	XR_007060527.1	n.179-725A>G		intron_variant, non_coding_transcript_variant
LOC105375508	XR_927976.3	n.179-725A>G		intron_variant, non_coding_transcript_variant
LOC105375508	XR_927977.3	n.178+44105A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96226 AN: 151884 Hom.: 31971 Cov.: 31

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.634 AC: 96312 AN: 152002 Hom.: 32010 Cov.: 31 AF XY: 0.636 AC XY: 47249 AN XY: 74306

Gnomad4 AFR AF: 0.840

Gnomad4 AMR AF: 0.629

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.699

Gnomad4 SAS AF: 0.614

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.616

Alfa AF: 0.547 Hom.: 34686

Bravo AF: 0.650

Asia WGS AF: 0.635 AC: 2207 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.8
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs972283; hg19: chr7-130466854;