chr7-24197136-C-T

Variant names:

• chr7-24197136-C-T
• rs156293
• ENST00000439839.1:n.160-107G>A

Variant summary

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

The ENST00000439839.1(ENSG00000228944):​n.160-107G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 151,732 control chromosomes in the GnomAD database, including 9,656 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 0.33 (9656 hom., cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000228944 ENST00000439839.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660
• Publications: 4 publications found

Genes affected

ENSG00000228944 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986777	XR_001745121.2	n.210-107G>A		intron_variant	Intron 2 of 2
LOC107986777	XR_001745122.2	n.81-107G>A		intron_variant	Intron 1 of 1
LOC107986777	XR_001745123.2	n.210-107G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228944	ENST00000439839.1	n.160-107G>A		intron_variant	Intron 1 of 1	5
ENSG00000228944	ENST00000718234.1	n.320-107G>A		intron_variant	Intron 2 of 3
ENSG00000228944	ENST00000745512.1	n.342-107G>A		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50573 AN: 151614 Hom.: 9645 Cov.: 31

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.312

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.334 AC: 50615 AN: 151732 Hom.: 9656 Cov.: 31 AF XY: 0.339 AC XY: 25138 AN XY: 74128

African (AFR) AF: 0.507 AC: 20957 AN: 41336

American (AMR) AF: 0.350 AC: 5336 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 657 AN: 3466

East Asian (EAS) AF: 0.477 AC: 2453 AN: 5138

South Asian (SAS) AF: 0.419 AC: 2003 AN: 4784

European-Finnish (FIN) AF: 0.255 AC: 2691 AN: 10538

Middle Eastern (MID) AF: 0.236 AC: 69 AN: 292

European-Non Finnish (NFE) AF: 0.231 AC: 15660 AN: 67928

Other (OTH) AF: 0.309 AC: 649 AN: 2102

Alfa AF: 0.297 Hom.: 1292

Bravo AF: 0.349

Asia WGS AF: 0.440 AC: 1530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.34
PhyloP100		-0.066

Splicing

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

Other links and lift over

dbSNP: rs156293; hg19: chr7-24236755;