rs7438808

chr4-69050666-G-T

Variant summary

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

The XR_001741714.2(LOC105377265):n.3048-530C>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 0.461 in 151,972 control chromosomes in the GnomAD database, including 17,602 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 0.46 (17602 hom., cov: 32)
• Consequence: LOC105377265 XR_001741714.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

LOC105377265 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377265	XR_001741714.2	n.3048-530C>A		intron_variant, non_coding_transcript_variant
LOC105377265	XR_938851.2	n.316-530C>A		intron_variant, non_coding_transcript_variant
LOC105377265	XR_938852.2	n.316-638C>A		intron_variant, non_coding_transcript_variant
LOC105377265	XR_938854.2	n.298-530C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.461 AC: 70013 AN: 151856 Hom.: 17579 Cov.: 32

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.461 AC: 70078 AN: 151972 Hom.: 17602 Cov.: 32 AF XY: 0.461 AC XY: 34272 AN XY: 74300

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.576

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.358

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.467

Alfa AF: 0.386 Hom.: 12256

Bravo AF: 0.475

Asia WGS AF: 0.478 AC: 1658 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.48
Dann	Benign	0.15

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7438808; hg19: chr4-69916384;