7-45970501-C-G

Variant names:

• chr7-45970501-C-G
• rs10260816
• ENST00000416708.1:n.153+692C>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000416708.1(ENSG00000237471):​n.153+692C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 151,922 control chromosomes in the GnomAD database, including 14,061 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 0.42 (14061 hom., cov: 32)
• Consequence: ENSG00000237471 ENST00000416708.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497

Genes affected

ENSG00000237471 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723446	NR_187744.1	n.433-7849C>G		intron_variant	Intron 1 of 3
LOC102723446	NR_187745.1	n.433-7018C>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000237471	ENST00000416708.1	n.153+692C>G		intron_variant	Intron 1 of 2	4
ENSG00000237471	ENST00000658576.1	n.165-7849C>G		intron_variant	Intron 1 of 3
ENSG00000237471	ENST00000664963.1	n.433-7018C>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64079 AN: 151804 Hom.: 14073 Cov.: 32

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.422 AC: 64086 AN: 151922 Hom.: 14061 Cov.: 32 AF XY: 0.418 AC XY: 31049 AN XY: 74248

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.539

Gnomad4 EAS AF: 0.759

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.435

Alfa AF: 0.237 Hom.: 473

Bravo AF: 0.424

Asia WGS AF: 0.525 AC: 1826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10260816; hg19: chr7-46010100;