4-76846492-C-T

Variant names:

• chr4-76846492-C-T
• rs1994854
• XM_047416557.1:c.145-1730C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047416557.1(LOC124900866):​c.145-1730C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,030 control chromosomes in the GnomAD database, including 2,527 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 0.18 (2527 hom., cov: 32)
• Consequence: LOC124900866 XM_047416557.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708
• Publications: 4 publications found

Genes affected

LOC124900866 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900866	XM_047416557.1	c.145-1730C>T		intron_variant	Intron 1 of 2		XP_047272513.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26771 AN: 151912 Hom.: 2511 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.176 AC: 26818 AN: 152030 Hom.: 2527 Cov.: 32 AF XY: 0.175 AC XY: 12995 AN XY: 74294

African (AFR) AF: 0.208 AC: 8606 AN: 41436

American (AMR) AF: 0.130 AC: 1978 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 880 AN: 3470

East Asian (EAS) AF: 0.109 AC: 565 AN: 5182

South Asian (SAS) AF: 0.249 AC: 1202 AN: 4818

European-Finnish (FIN) AF: 0.124 AC: 1304 AN: 10558

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.172 AC: 11688 AN: 67992

Other (OTH) AF: 0.185 AC: 390 AN: 2108

Alfa AF: 0.174 Hom.: 3466

Bravo AF: 0.178

Asia WGS AF: 0.164 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.2
DANN	Benign	0.41
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs1994854; hg19: chr4-77767645;