7-99941218-A-G

Variant names:

• chr7-99941218-A-G
• rs2527894
• ENST00000456499.1:n.328-2757A>G

Variant summary

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

The ENST00000456499.1(ENSG00000237640):​n.328-2757A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 152,124 control chromosomes in the GnomAD database, including 32,690 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 0.64 (32690 hom., cov: 33)
• Consequence: ENSG00000237640 ENST00000456499.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59
• Publications: 7 publications found

Genes affected

ENSG00000237640 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456499.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000237640	ENST00000456499.1	TSL:3	n.328-2757A>G		intron	N/A
	ENSG00000237640	ENST00000790901.1		n.381-2757A>G		intron	N/A
	ENSG00000237640	ENST00000790904.1		n.173-3241A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.639 AC: 97110 AN: 152006 Hom.: 32640 Cov.: 33

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.639 AC: 97215 AN: 152124 Hom.: 32690 Cov.: 33 AF XY: 0.634 AC XY: 47112 AN XY: 74352

African (AFR) AF: 0.858 AC: 35636 AN: 41536

American (AMR) AF: 0.532 AC: 8144 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1775 AN: 3472

East Asian (EAS) AF: 0.317 AC: 1628 AN: 5142

South Asian (SAS) AF: 0.553 AC: 2660 AN: 4810

European-Finnish (FIN) AF: 0.606 AC: 6407 AN: 10576

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.577 AC: 39198 AN: 67978

Other (OTH) AF: 0.598 AC: 1263 AN: 2112

Alfa AF: 0.607 Hom.: 48923

Bravo AF: 0.640

Asia WGS AF: 0.508 AC: 1767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.66
DANN	Benign	0.23
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs2527894; hg19: chr7-99538841;