1-241847325-C-G

Variant names:

• chr1-241847325-C-G
• rs10802996
• ENST00000684005.2:n.168+644G>C

Variant summary

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

The ENST00000684005.2(ENSG00000288723):​n.168+644G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 152,036 control chromosomes in the GnomAD database, including 4,109 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 0.21 (4109 hom., cov: 32)
• Consequence: ENSG00000288723 ENST00000684005.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.248
• Publications: 15 publications found

Genes affected

ENSG00000288723 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.29 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
ENSG00000288723	ENST00000684005.2	n.168+644G>C		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32556 AN: 151918 Hom.: 4109 Cov.: 32

Gnomad AFR AF: 0.0800

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.214 AC: 32553 AN: 152036 Hom.: 4109 Cov.: 32 AF XY: 0.217 AC XY: 16102 AN XY: 74296

African (AFR) AF: 0.0799 AC: 3318 AN: 41510

American (AMR) AF: 0.297 AC: 4543 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 733 AN: 3470

East Asian (EAS) AF: 0.210 AC: 1083 AN: 5166

South Asian (SAS) AF: 0.281 AC: 1351 AN: 4812

European-Finnish (FIN) AF: 0.294 AC: 3091 AN: 10530

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17691 AN: 67960

Other (OTH) AF: 0.213 AC: 450 AN: 2110

Alfa AF: 0.151 Hom.: 330

Bravo AF: 0.209

Asia WGS AF: 0.237 AC: 826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.6
DANN	Benign	0.61
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs10802996; hg19: chr1-242010627;