1-202960413-C-G

Variant names:

• chr1-202960413-C-G
• rs7523903
• ENST00000823934.1:n.202+1750C>G

Variant summary

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

The ENST00000823934.1(ENSG00000307108):​n.202+1750C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0803 in 152,224 control chromosomes in the GnomAD database, including 1,231 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 0.080 (1231 hom., cov: 32)
• Consequence: ENSG00000307108 ENST00000823934.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188
• Publications: 3 publications found

Genes affected

ENSG00000307108 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000823934.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307108	ENST00000823934.1		n.202+1750C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0801 AC: 12181 AN: 152106 Hom.: 1217 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0360

Gnomad ASJ AF: 0.00346

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.0988

Gnomad FIN AF: 0.00311

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00663

Gnomad OTH AF: 0.0656

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

GnomAD4 genome AF: 0.0803 AC: 12228 AN: 152224 Hom.: 1231 Cov.: 32 AF XY: 0.0809 AC XY: 6020 AN XY: 74418

African (AFR) AF: 0.228 AC: 9461 AN: 41504

American (AMR) AF: 0.0362 AC: 553 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00346 AC: 12 AN: 3470

East Asian (EAS) AF: 0.208 AC: 1078 AN: 5176

South Asian (SAS) AF: 0.0982 AC: 474 AN: 4826

European-Finnish (FIN) AF: 0.00311 AC: 33 AN: 10608

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.00664 AC: 452 AN: 68026

Other (OTH) AF: 0.0724 AC: 153 AN: 2112

Alfa AF: 0.00926 Hom.: 11

Bravo AF: 0.0884

Asia WGS AF: 0.154 AC: 535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.50
DANN	Benign	0.82
PhyloP100		-0.19

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7523903;

hg19: chr1-202929541;