rs7787204

Variant names:

• chr7-9807667-A-G
• rs7787204
• ENST00000731005.1:n.279-47604T>C

Variant summary

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

The ENST00000731005.1(ENSG00000295572):​n.279-47604T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0909 in 152,072 control chromosomes in the GnomAD database, including 732 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 0.091 (732 hom., cov: 33)
• Consequence: ENSG00000295572 ENST00000731005.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355
• Publications: 3 publications found

Genes affected

ENSG00000295572 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375147	XR_927026.2	n.210-47604T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295572	ENST00000731005.1	n.279-47604T>C		intron_variant	Intron 2 of 3
ENSG00000295572	ENST00000731006.1	n.170-14109T>C		intron_variant	Intron 2 of 4
ENSG00000295572	ENST00000731007.1	n.242-47604T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0909 AC: 13812 AN: 151956 Hom.: 727 Cov.: 33

Gnomad AFR AF: 0.0715

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.0595

Gnomad ASJ AF: 0.0962

Gnomad EAS AF: 0.00328

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0791

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

GnomAD4 genome AF: 0.0909 AC: 13830 AN: 152072 Hom.: 732 Cov.: 33 AF XY: 0.0914 AC XY: 6795 AN XY: 74338

African (AFR) AF: 0.0716 AC: 2968 AN: 41480

American (AMR) AF: 0.0594 AC: 908 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0962 AC: 334 AN: 3472

East Asian (EAS) AF: 0.00328 AC: 17 AN: 5176

South Asian (SAS) AF: 0.113 AC: 547 AN: 4822

European-Finnish (FIN) AF: 0.117 AC: 1232 AN: 10574

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7547 AN: 67962

Other (OTH) AF: 0.0821 AC: 173 AN: 2106

Alfa AF: 0.104 Hom.: 643

Bravo AF: 0.0840

Asia WGS AF: 0.0660 AC: 229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.47
DANN	Benign	0.35
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs7787204; hg19: chr7-9847296;