rs2214310

Variant names:

• chr7-25339244-G-A
• rs2214310
• ENST00000718235.1:n.398+5734C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-25339244-G-A
• chr7-25339244-G-C
• chr7-25339244-G-T

Variant summary

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

The ENST00000718235.1(ENSG00000233824):​n.398+5734C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 152,088 control chromosomes in the GnomAD database, including 23,502 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 0.55 (23502 hom., cov: 33)
• Consequence: ENSG00000233824 ENST00000718235.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 3 publications found

Genes affected

ENSG00000233824 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718235.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000233824	ENST00000718235.1		n.398+5734C>T		intron	N/A
	ENSG00000233824	ENST00000765804.1		n.380+5734C>T		intron	N/A
	ENSG00000233824	ENST00000765805.1		n.435+5734C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83737 AN: 151970 Hom.: 23483 Cov.: 33

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.551 AC: 83802 AN: 152088 Hom.: 23502 Cov.: 33 AF XY: 0.549 AC XY: 40775 AN XY: 74324

African (AFR) AF: 0.658 AC: 27311 AN: 41512

American (AMR) AF: 0.521 AC: 7972 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1848 AN: 3468

East Asian (EAS) AF: 0.519 AC: 2678 AN: 5160

South Asian (SAS) AF: 0.441 AC: 2116 AN: 4800

European-Finnish (FIN) AF: 0.469 AC: 4960 AN: 10572

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.516 AC: 35055 AN: 67976

Other (OTH) AF: 0.567 AC: 1197 AN: 2112

Alfa AF: 0.537 Hom.: 33173

Bravo AF: 0.564

Asia WGS AF: 0.489 AC: 1703 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.80
DANN	Benign	0.42
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs2214310; hg19: chr7-25378863;