4-66950161-C-G

Variant names:

• chr4-66950161-C-G
• rs1435431
• XR_938847.2:n.345-79314G>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_938847.2(LOC105377262):​n.345-79314G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 151,994 control chromosomes in the GnomAD database, including 5,195 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 0.24 (5195 hom., cov: 32)
• Consequence: LOC105377262 XR_938847.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 1 publications found

Genes affected

LOC105377262 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377262	XR_938847.2	n.345-79314G>C		intron_variant	Intron 1 of 3
LOC105377262	XR_938848.2	n.345-79314G>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36740 AN: 151874 Hom.: 5191 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.0688

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.242 AC: 36772 AN: 151994 Hom.: 5195 Cov.: 32 AF XY: 0.242 AC XY: 17997 AN XY: 74284

African (AFR) AF: 0.375 AC: 15540 AN: 41446

American (AMR) AF: 0.155 AC: 2358 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 909 AN: 3470

East Asian (EAS) AF: 0.0686 AC: 355 AN: 5176

South Asian (SAS) AF: 0.346 AC: 1665 AN: 4810

European-Finnish (FIN) AF: 0.210 AC: 2218 AN: 10578

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13052 AN: 67942

Other (OTH) AF: 0.223 AC: 471 AN: 2110

Alfa AF: 0.126 Hom.: 218

Bravo AF: 0.239

Asia WGS AF: 0.200 AC: 697 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	20
DANN	Benign	0.66
PhyloP100		0.077

Splicing

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

Other links and lift over

dbSNP: rs1435431; hg19: chr4-67815879;