9-112168826-G-T

Variant names:

• chr9-112168826-G-T
• rs4979085
• NM_022486.5:c.103+6307C>A

Variant summary

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

The NM_022486.5(SUSD1):​c.103+6307C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 151,998 control chromosomes in the GnomAD database, including 6,674 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 0.27 (6674 hom., cov: 32)
• Consequence: SUSD1 NM_022486.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.483
• Publications: 10 publications found

Genes affected

SUSD1 (HGNC:25413): (sushi domain containing 1) Predicted to enable calcium ion binding activity. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUSD1	NM_022486.5	c.103+6307C>A		intron_variant	Intron 1 of 16	ENST00000374270.8	NP_071931.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUSD1	ENST00000374270.8	c.103+6307C>A		intron_variant	Intron 1 of 16	1	NM_022486.5	ENSP00000363388.4
SUSD1	ENST00000374264.6	c.103+6307C>A		intron_variant	Intron 1 of 17	1		ENSP00000363382.2
SUSD1	ENST00000374263.7	c.103+6307C>A		intron_variant	Intron 1 of 15	2		ENSP00000363381.3
SUSD1	ENST00000355396.7	c.52+6307C>A		intron_variant	Intron 1 of 15	2		ENSP00000347558.3

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40839 AN: 151880 Hom.: 6677 Cov.: 32

Gnomad AFR AF: 0.0789

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.269 AC: 40840 AN: 151998 Hom.: 6674 Cov.: 32 AF XY: 0.275 AC XY: 20414 AN XY: 74278

African (AFR) AF: 0.0789 AC: 3274 AN: 41508

American (AMR) AF: 0.318 AC: 4858 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1333 AN: 3470

East Asian (EAS) AF: 0.300 AC: 1551 AN: 5162

South Asian (SAS) AF: 0.337 AC: 1625 AN: 4818

European-Finnish (FIN) AF: 0.457 AC: 4815 AN: 10532

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22354 AN: 67940

Other (OTH) AF: 0.313 AC: 662 AN: 2112

Alfa AF: 0.293 Hom.: 3526

Bravo AF: 0.254

Asia WGS AF: 0.295 AC: 1026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.74
PhyloP100		0.48
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs4979085; hg19: chr9-114931106;