rs4675644

Variant names:

• chr2-206975608-G-C
• rs4675644
• ENST00000762203.1:n.109-60874C>G

Variant summary

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

The ENST00000762203.1(ENSG00000299281):​n.109-60874C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 152,090 control chromosomes in the GnomAD database, including 5,842 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 0.26 (5842 hom., cov: 32)
• Consequence: ENSG00000299281 ENST00000762203.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640
• Publications: 7 publications found

Genes affected

ENSG00000299281 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762203.1. 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
	ENSG00000299281	ENST00000762203.1		n.109-60874C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40078 AN: 151972 Hom.: 5828 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.264 AC: 40149 AN: 152090 Hom.: 5842 Cov.: 32 AF XY: 0.262 AC XY: 19445 AN XY: 74340

African (AFR) AF: 0.376 AC: 15602 AN: 41484

American (AMR) AF: 0.286 AC: 4372 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 794 AN: 3470

East Asian (EAS) AF: 0.200 AC: 1031 AN: 5166

South Asian (SAS) AF: 0.263 AC: 1264 AN: 4802

European-Finnish (FIN) AF: 0.148 AC: 1562 AN: 10584

Middle Eastern (MID) AF: 0.175 AC: 51 AN: 292

European-Non Finnish (NFE) AF: 0.216 AC: 14700 AN: 67990

Other (OTH) AF: 0.257 AC: 542 AN: 2110

Alfa AF: 0.231 Hom.: 2416

Bravo AF: 0.279

Asia WGS AF: 0.270 AC: 941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.37
PhyloP100		-0.064

Splicing

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

Other links and lift over

dbSNP: rs4675644; hg19: chr2-207840332;