rs7435274

Positions:

• chr4-69050281-A-C
• chr4-69050281-A-T

Variant summary

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

The XR_001741714.2(LOC105377265):​n.3048-145T>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 0.461 in 151,992 control chromosomes in the GnomAD database, including 17,583 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 (17583 hom., cov: 32)
• Consequence: LOC105377265 XR_001741714.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.19

Genes affected

LOC105377265 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.13).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377265	XR_001741714.2	n.3048-145T>G		intron_variant, non_coding_transcript_variant
LOC105377265	XR_938851.2	n.316-145T>G		intron_variant, non_coding_transcript_variant
LOC105377265	XR_938852.2	n.316-253T>G		intron_variant, non_coding_transcript_variant
LOC105377265	XR_938854.2	n.298-145T>G		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: 69966 AN: 151872 Hom.: 17558 Cov.: 32

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.357

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: 70035 AN: 151992 Hom.: 17583 Cov.: 32 AF XY: 0.461 AC XY: 34230 AN XY: 74288

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.513

Gnomad4 EAS AF: 0.575

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.467

Alfa AF: 0.219 Hom.: 438

Bravo AF: 0.475

Asia WGS AF: 0.479 AC: 1661 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	0.27
DANN	Benign	0.16

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: rs7435274; hg19: chr4-69915999;