rs7628219

Positions:

• chr3-70577209-C-T

Variant summary

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

The XR_001740559.2(LOC105377152):​n.367-1256G>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 0.152 in 151,680 control chromosomes in the GnomAD database, including 1,967 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 0.15 (1967 hom., cov: 32)
• Consequence: LOC105377152 XR_001740559.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.421

Genes affected

LOC105377152 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377152	XR_001740559.2	n.367-1256G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.152 AC: 22986 AN: 151560 Hom.: 1969 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.0282

Gnomad SAS AF: 0.0686

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.152 AC: 22995 AN: 151680 Hom.: 1967 Cov.: 32 AF XY: 0.148 AC XY: 10990 AN XY: 74112

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.0281

Gnomad4 SAS AF: 0.0685

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.158

Alfa AF: 0.144 Hom.: 1495

Bravo AF: 0.159

Asia WGS AF: 0.0680 AC: 238 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7628219; hg19: chr3-70626360;