rs4976028

Variant names:

• chr5-67994905-A-G
• rs4976028
• ENST00000785994.1:n.48+76T>C

Your query was ambiguous. Multiple possible variants found:

• chr5-67994905-A-G
• chr5-67994905-A-T

Variant summary

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

The ENST00000785994.1(ENSG00000302346):​n.48+76T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,158 control chromosomes in the GnomAD database, including 3,230 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 0.19 (3230 hom., cov: 32)
• Consequence: ENSG00000302346 ENST00000785994.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157
• Publications: 5 publications found

Genes affected

ENSG00000302346 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302346	ENST00000785994.1	n.48+76T>C		intron_variant	Intron 1 of 5
ENSG00000302346	ENST00000785996.1	n.370-9710T>C		intron_variant	Intron 1 of 3
ENSG00000302346	ENST00000785997.1	n.112+3592T>C		intron_variant	Intron 1 of 3
ENSG00000302346	ENST00000785998.1	n.342+76T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28222 AN: 152040 Hom.: 3233 Cov.: 32

Gnomad AFR AF: 0.0584

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.0434

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.185 AC: 28225 AN: 152158 Hom.: 3230 Cov.: 32 AF XY: 0.183 AC XY: 13640 AN XY: 74380

African (AFR) AF: 0.0583 AC: 2422 AN: 41524

American (AMR) AF: 0.224 AC: 3422 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 770 AN: 3472

East Asian (EAS) AF: 0.0433 AC: 224 AN: 5178

South Asian (SAS) AF: 0.148 AC: 715 AN: 4824

European-Finnish (FIN) AF: 0.233 AC: 2467 AN: 10592

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.258 AC: 17567 AN: 67970

Other (OTH) AF: 0.191 AC: 404 AN: 2112

Alfa AF: 0.237 Hom.: 3760

Bravo AF: 0.180

Asia WGS AF: 0.110 AC: 381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.9
DANN	Benign	0.50
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs4976028; hg19: chr5-67290733;