rs7703021

Variant names:

• chr5-92635591-A-G
• rs7703021
• ENST00000512210.5:n.52+3855T>C

Variant summary

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

The ENST00000512210.5(ENSG00000249776):​n.52+3855T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,158 control chromosomes in the GnomAD database, including 1,721 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 0.14 (1721 hom., cov: 32)
• Consequence: ENSG00000249776 ENST00000512210.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.83
• Publications: 2 publications found

Genes affected

ENSG00000249776 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379082	NR_188296.1	n.362+34161T>C		intron_variant	Intron 3 of 3
LOC105379082	NR_188297.1	n.217+35893T>C		intron_variant	Intron 2 of 2
LOC105379082	NR_188298.1	n.217+35893T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249776	ENST00000512210.5	n.52+3855T>C		intron_variant	Intron 1 of 3	3
ENSG00000249776	ENST00000513779.1	n.134+25139T>C		intron_variant	Intron 1 of 2	3
ENSG00000249776	ENST00000718057.1	n.390+34161T>C		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21925 AN: 152042 Hom.: 1719 Cov.: 32

Gnomad AFR AF: 0.0745

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.0284

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.144 AC: 21925 AN: 152158 Hom.: 1721 Cov.: 32 AF XY: 0.142 AC XY: 10531 AN XY: 74388

African (AFR) AF: 0.0744 AC: 3090 AN: 41538

American (AMR) AF: 0.204 AC: 3117 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 645 AN: 3462

East Asian (EAS) AF: 0.0286 AC: 148 AN: 5168

South Asian (SAS) AF: 0.178 AC: 859 AN: 4816

European-Finnish (FIN) AF: 0.130 AC: 1376 AN: 10598

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.179 AC: 12136 AN: 67982

Other (OTH) AF: 0.161 AC: 340 AN: 2112

Alfa AF: 0.175 Hom.: 1904

Bravo AF: 0.147

Asia WGS AF: 0.121 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	16
DANN	Benign	0.84
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs7703021; hg19: chr5-91971298;