rs7644516

Positions:

• chr3-25880794-G-A

Variant summary

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

The XR_007095849.1(LOC124909357):​n.226+6791G>A 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 0.926 in 152,306 control chromosomes in the GnomAD database, including 65,413 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 0.93 (65413 hom., cov: 33)
• Consequence: LOC124909357 XR_007095849.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.412

Genes affected

LOC124909357 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124909357	XR_007095849.1	n.226+6791G>A		intron_variant, non_coding_transcript_variant
LOC124909357	XR_007095848.1	n.123+6894G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.926 AC: 140881 AN: 152188 Hom.: 65350 Cov.: 33

Gnomad AFR AF: 0.978

Gnomad AMI AF: 0.883

Gnomad AMR AF: 0.920

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.941

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.925

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

GnomAD4 genome AF: 0.926 AC: 141006 AN: 152306 Hom.: 65413 Cov.: 33 AF XY: 0.928 AC XY: 69086 AN XY: 74462

Gnomad4 AFR AF: 0.978

Gnomad4 AMR AF: 0.920

Gnomad4 ASJ AF: 0.908

Gnomad4 EAS AF: 0.987

Gnomad4 SAS AF: 0.881

Gnomad4 FIN AF: 0.941

Gnomad4 NFE AF: 0.892

Gnomad4 OTH AF: 0.926

Alfa AF: 0.901 Hom.: 31888

Bravo AF: 0.926

Asia WGS AF: 0.922 AC: 3201 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.3
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7644516; hg19: chr3-25922285;