rs1440971

Variant names:

• chr7-127632346-A-G
• rs1440971
• ENST00000787994.1:n.760+10512A>G

Variant summary

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

The ENST00000787994.1(ENSG00000302590):​n.760+10512A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,094 control chromosomes in the GnomAD database, including 3,038 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 0.19 (3038 hom., cov: 31)
• Consequence: ENSG00000302590 ENST00000787994.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.356
• Publications: 6 publications found

Genes affected

ENSG00000302590 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.261 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
ENSG00000302590	ENST00000787994.1	n.760+10512A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29489 AN: 151976 Hom.: 3038 Cov.: 31

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.194 AC: 29502 AN: 152094 Hom.: 3038 Cov.: 31 AF XY: 0.194 AC XY: 14436 AN XY: 74364

African (AFR) AF: 0.265 AC: 10990 AN: 41464

American (AMR) AF: 0.160 AC: 2437 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 461 AN: 3470

East Asian (EAS) AF: 0.124 AC: 638 AN: 5158

South Asian (SAS) AF: 0.250 AC: 1205 AN: 4816

European-Finnish (FIN) AF: 0.167 AC: 1774 AN: 10596

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

European-Non Finnish (NFE) AF: 0.169 AC: 11482 AN: 68000

Other (OTH) AF: 0.177 AC: 374 AN: 2110

Alfa AF: 0.180 Hom.: 2102

Bravo AF: 0.194

Asia WGS AF: 0.166 AC: 579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.5
DANN	Benign	0.83
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs1440971; hg19: chr7-127272400;