rs60111824

Variant names:

• chr7-6734504-A-G
• rs60111824
• ENST00000486256.5:n.749-801A>G

Variant summary

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

The ENST00000486256.5(ENSG00000290835):​n.749-801A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 151,962 control chromosomes in the GnomAD database, including 3,915 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 0.17 (3915 hom., cov: 32)
• Consequence: ENSG00000290835 ENST00000486256.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108
• Publications: 4 publications found

Genes affected

ENSG00000290835 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 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
ENSG00000290835	ENST00000486256.5	n.749-801A>G		intron_variant	Intron 7 of 13	1
ENSG00000290835	ENST00000716284.1	n.1855-801A>G		intron_variant	Intron 7 of 12
ENSG00000290835	ENST00000716285.1	n.478-801A>G		intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25040 AN: 151846 Hom.: 3910 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0701

Gnomad EAS AF: 0.00406

Gnomad SAS AF: 0.0931

Gnomad FIN AF: 0.0337

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.0700

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.165 AC: 25079 AN: 151962 Hom.: 3915 Cov.: 32 AF XY: 0.160 AC XY: 11904 AN XY: 74292

African (AFR) AF: 0.414 AC: 17122 AN: 41404

American (AMR) AF: 0.111 AC: 1700 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0701 AC: 243 AN: 3466

East Asian (EAS) AF: 0.00407 AC: 21 AN: 5154

South Asian (SAS) AF: 0.0932 AC: 447 AN: 4798

European-Finnish (FIN) AF: 0.0337 AC: 357 AN: 10590

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.0699 AC: 4753 AN: 67962

Other (OTH) AF: 0.146 AC: 308 AN: 2114

Alfa AF: 0.125 Hom.: 316

Bravo AF: 0.180

Asia WGS AF: 0.0650 AC: 227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.4
DANN	Benign	0.17
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs60111824; hg19: chr7-6774135;