rs7672521

Positions:

• chr4-174381022-C-T

Variant summary

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

The XR_939487.2(LOC105377547):​n.842-7555C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0785 in 152,206 control chromosomes in the GnomAD database, including 635 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 0.078 (635 hom., cov: 32)
• Consequence: LOC105377547 XR_939487.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274

Genes affected

LOC105377547 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377547	XR_001741919.1	n.842-7555C>T		intron_variant
LOC105377547	XR_001741920.1	n.211-7555C>T		intron_variant
LOC105377547	XR_939487.2	n.842-7555C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0784 AC: 11929 AN: 152088 Hom.: 633 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0334

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0668

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0422

Gnomad OTH AF: 0.0649

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

GnomAD4 genome AF: 0.0785 AC: 11943 AN: 152206 Hom.: 635 Cov.: 32 AF XY: 0.0822 AC XY: 6115 AN XY: 74420

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.0334

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.0668

Gnomad4 NFE AF: 0.0422

Gnomad4 OTH AF: 0.0685

Alfa AF: 0.0659 Hom.: 111

Bravo AF: 0.0834

Asia WGS AF: 0.181 AC: 627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.91
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7672521; hg19: chr4-175302173;