chr4-174379628-T-C

Position:

• chr4-174379628-T-C

Variant summary

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

The XR_001741920.1(LOC105377547):​n.211-8949T>C 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 0.166 in 152,146 control chromosomes in the GnomAD database, including 2,494 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 0.17 (2494 hom., cov: 32)
• Consequence: LOC105377547 XR_001741920.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

Genes affected

LOC105377547 (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 = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377547	XR_001741920.1	n.211-8949T>C		intron_variant, non_coding_transcript_variant
LOC105377547	XR_001741919.1	n.842-8949T>C		intron_variant, non_coding_transcript_variant
LOC105377547	XR_939487.2	n.842-8949T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25276 AN: 152028 Hom.: 2493 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.166 AC: 25289 AN: 152146 Hom.: 2494 Cov.: 32 AF XY: 0.166 AC XY: 12340 AN XY: 74380

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.509

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.153

Alfa AF: 0.159 Hom.: 1773

Bravo AF: 0.175

Asia WGS AF: 0.267 AC: 929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.22
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6852435; hg19: chr4-175300779;